Well... sorry to comment so late, but as a professional in the tourist business, I guess I should.
Most important thing first:
Berlin is big. 892 square kilometer big. Use public transport, or rent a bike.
Tours:
Bus tours, Ok for a general overview.
Boat tours, avoid the piddly one hour inner city tours, unless you've got no time. General consensus is that the "Grosse Brückenfahrt" tours are best, but somewhat longish at three hours.
Walking Tours, too many to comment on. Usually somewhat limited in range.
Guided bike tours (rental included, if needed), recommended, especially Berlin on Bike, inside the Kulturbrauerei, close to Eberswalder Strasse station on subway line 2. Usually feature quite a few interesting "behind the scenes" locations.
Guided tours in a bicycle rikshaw, very recommended if pricey, but the driver usually can find a tour to fit your interests, or improvise one off the beaten paths. Alternatively, for groups of 4-6 people, tours on Conference Bikes, usually off Brandenburg Gate.
Sights:
TV tower, pricey and waiting times up to several hours. Not really recommended.
Kohlhoff tower at Potsdamer Platz, a lot cheaper, no waiting time, still a nice view.
Siegessäule inside Tiergarten park, great view, 285 steps up, though.
Zionskirche in Prenzlauer Berg district, accessible for a donation, good view.
Kreuzberg inside Viktoriapark, free, great view, inside the most beautiful "Gründerzeit" (early Wilhelminian era) Park of Berlin. Unfortunately, the waterfall is likely still offline. Bonus: walk down Methfesselstrasse for a memorial to the first computer manufactory of the world.
Radio Tower, good view, easy to get to via Ringbahn S4[12].
Museums:
Pergamon and Neues Museum on museum island. Naturkundemuseum at Invalidenstrasse east of Hauptbahnhof. Ramones Museum at Krausnickstrasse, near the new synagoge. Hanfmuseum at Mühlendamm, Nikolai quarter.
Eat:
Berlin is a city with a lot of fast food culture. Most Berliners don't include McDonalds/Burger King & Co. in the "culture" part though.
Curry 36, Habibi's at subway station Mehringdamm, lines 6,7.
Small pancake/potato fritter stand aside the big department store on Hermannplatz, subway lines 7,8.
Borchardt, Französische Strasse (suit not needed, but fursuit not recommended, reserve on weekend evenings)
Zoos:
Berlin Zoo, near Zoo station: recommended on weekdays (but often overly full on weekends).
Tierpark, near Tierpark Station, subway line 5: a lot more space here, also recommended on weekends.
HTH